ORM1

orosomucoid 1, the group of Lipocalins

Basic information

Region (hg38): 9:114323097-114326479

Links

ENSG00000229314 ∙ NCBI:5004 ∙ OMIM:138600 ∙ HGNC:8498 ∙ Uniprot:P02763 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ORM1 gene.

• Inborn genetic diseases (3 variants)
• - (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORM1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in ORM1

This is a list of pathogenic ClinVar variants found in the ORM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-114323246-G-A			Benign (Dec 31, 2019)
9-114323246-G-G		-	no classification for the single variant (-)
9-114323732-A-G		not specified	Uncertain significance (Dec 15, 2022)
9-114324046-T-G		not specified	Uncertain significance (Oct 03, 2023)
9-114324062-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-114324076-A-G		not specified	Uncertain significance (Mar 24, 2023)
9-114324838-A-G		not specified	Uncertain significance (Dec 13, 2023)
9-114325064-C-T		not specified	Uncertain significance (Aug 02, 2022)
9-114325132-G-A		-	no classification for the single variant (-)
9-114325132-G-G		-	no classification for the single variant (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ORM1	protein_coding	protein_coding	ENST00000259396	6	3420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000115	0.604	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.339	116	106	1.09	0.00000618	1271
Missense in Polyphen		28	32.723	0.85568		407
Synonymous	-1.58	61	47.2	1.29	0.00000330	355
Loss of Function	0.840	9	12.2	0.740	6.72e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as transport protein in the blood stream. Binds various ligands in the interior of its beta-barrel domain. Also binds synthetic drugs and influences their distribution and availability in the body. Appears to function in modulating the activity of the immune system during the acute-phase reaction. {ECO:0000269|PubMed:17008009, ECO:0000269|PubMed:17321687}.
• Pathway: Vitamin D Receptor Pathway;Neutrophil degranulation;Innate Immune System;Immune System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.317

Intolerance Scores

• loftool: 0.855
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.178
• hipred: N
• hipred_score: 0.195
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.725

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Gene ontology

• Biological process: platelet degranulation;regulation of immune system process;acute-phase response;inflammatory response;negative regulation of interleukin-6 production;negative regulation of tumor necrosis factor production;neutrophil degranulation;positive regulation of interleukin-1 secretion;positive regulation of interleukin-1 beta secretion;positive regulation of tumor necrosis factor secretion
• Cellular component: extracellular region;extracellular space;platelet alpha granule lumen;specific granule lumen;collagen-containing extracellular matrix;extracellular exosome;blood microparticle;tertiary granule lumen
• Molecular function: protein binding